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Genetics and Breeding of Forage
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Genetics and Breeding of Forage

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: closed (5 September 2025) | Viewed by 2531

Special Issue Editors

Prof. Dr. Maofeng Chai

E-Mail Website
Guest Editor
College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China
Interests: forage breeding; molecular biology; seed dormancy; abiotic stress; leaf senescence
Dr. Zhenyi Li

E-Mail Website
Guest Editor
College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot 010000, China
Interests: alfalfa; forage molecular breeding; functional biology; salt resistance; phosphate deficiency response

Special Issue Information

Dear Colleagues,

Forage is crucial for animal feed and is a fundamental component of grasslands worldwide. As human populations grow and the global environment changes, there is a need for a greater variety of forage to ensure sufficient protein for animals and to rejuvenate depleted pastures. Unlike crops, forage can be characterized by its various species, multiple reproductive types, perennial forms, strong wild characteristics, strong autumn dormancy, and difficulties in seed harvesting. Understanding the genetic characteristics of forage traits is beneficial for unlocking the excellent potential of the germplasm resource pool, thereby creating desirable varieties. Improving important agronomic traits, such as yield and quality, abiotic stress tolerance, nutrient utilization, and seed yield, can be achieved through traditional or biotechnology methods.

This Special Issue aims to provide a comprehensive and up-to-date overview of the "Genetics and Breeding of Forage". It focuses on understanding the genetic background of forage, its ability to adapt to adverse environmental conditions, genome-related research, changes in forage, and genetic functional analysis from multiple perspectives, such as plant physiology, genetics, functional genomics, and phenotype and germplasm development. This information will help enhance forage production, stress management, seed quality, and more.

Prof. Dr. Maofeng Chai
Dr. Zhenyi Li
Guest Editors

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Keywords

  • forage genetic improvement
  • molecular breeding
  • abiotic stress
  • biotic stress
  • population genetics
  • multi-omics analysis
  • nutrition absorption

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Published Papers (4 papers)

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Research

47 pages, 978 KB  
Article
Genetic Parameters, Prediction of Genotypic Values, and Forage Stability in Paspalum nicorae Parodi Ecotypes via REML/BLUP
by Diógenes Cecchin Silveira, Annamaria Mills, Júlio Antoniolli, Victor Schneider de Ávila, Maria Eduarda Pagani Sangineto, Juliana Medianeira Machado, Roberto Luis Weiler, André Pich Brunes, Carine Simioni and Miguel Dall’Agnol
Genes 2025, 16(10), 1164; https://doi.org/10.3390/genes16101164 - 1 Oct 2025
Viewed by 235
Abstract
Background/Objectives: Paspalum nicorae Parodi is a native subtropical grass species with promising agronomic attributes, such as persistence, drought and cold tolerance, and rapid establishment. However, the species remains underutilized in breeding programs due to the absence of well-characterized germplasm and limited studies on [...] Read more.
Background/Objectives: Paspalum nicorae Parodi is a native subtropical grass species with promising agronomic attributes, such as persistence, drought and cold tolerance, and rapid establishment. However, the species remains underutilized in breeding programs due to the absence of well-characterized germplasm and limited studies on its genetic variability and agronomic potential. This study aimed to estimate genetic parameters, predict genotypic values, and identify superior ecotypes with desirable forage traits, integrating stability and adaptability analyses. Methods: A total of 84 ecotypes were evaluated over three consecutive years for twelve morphological and forage-related traits. Genetic parameters, genotypic values, and selection gains were estimated using mixed models (REML/BLUP). Stability was assessed through harmonic means of genotypic performance, and the multi-trait genotype–ideotype distance index (MGIDI) was applied to identify ecotypes with balanced performance across traits. Results: Substantial genetic variability was detected for most traits, particularly those related to biomass accumulation, such as total dry matter, the number of tillers, fresh matter, and leaf dry matter. These traits exhibited medium to high heritability and strong potential for selection. Ecotype N3.10 consistently showed superior performance across productivity traits while other ecotypes, such as N4.14 and N1.09, stood out for quality-related attributes and cold tolerance, respectively. The application of the MGIDI index enabled the identification of 17 ecotypes with balanced multi-trait performance, supporting the simultaneous selection for productivity, quality, and adaptability. Comparisons with P. notatum suggest that P. nicorae harbors competitive genetic potential, despite its lower level of domestication. Conclusions: The integration of REML/BLUP analyses, stability parameters, and ideotype-based multi-trait selection provided a robust framework for identifying elite P. nicorae ecotypes. These findings reinforce the strategic importance of this species as a valuable genetic resource for the development of adapted and productive forage cultivars in subtropical environments. Full article
(This article belongs to the Special Issue Genetics and Breeding of Forage)
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14 pages, 1564 KB  
Article
MtSIN1a Enhances Salinity Tolerance in Medicago truncatula and Alfalfa
by Huanyu Yue, Yuxue Zhang, Yafei Liu, Feng Yuan, Chuanen Zhou and Yang Zhao
Genes 2025, 16(10), 1156; https://doi.org/10.3390/genes16101156 - 29 Sep 2025
Viewed by 291
Abstract
Background/Objectives: Alfalfa is a widely cultivated high-quality forage crop, and salinity tolerance is one of the most important breeding goals. Glycine max SALT INDUCED NAC 1 (GmSIN1) was found to enhance salinity tolerance in soybean plants. The phylogenetic analysis showed [...] Read more.
Background/Objectives: Alfalfa is a widely cultivated high-quality forage crop, and salinity tolerance is one of the most important breeding goals. Glycine max SALT INDUCED NAC 1 (GmSIN1) was found to enhance salinity tolerance in soybean plants. The phylogenetic analysis showed there were two homologs of GmSIN1 in Medicago truncatula, MtSIN1a and MtSIN1b. This raised questions regarding the roles of MtSIN1s in alfalfa under salinity stress. Methods: From a Tnt1 mutant collection, we identified the mutants of MtSIN1a. We recorded the survival rate and plant height of mtsin1a-1 and mtsin1a-2 after 100 mM NaCl treatment. Subsequently, we generated 35S:MtSIN1a-GFP transgenic alfalfa lines via genetic transformation. Two lines with relatively high MtSIN1a expression, 35S:MtSIN1a-GFP#3 and 35S:MtSIN1a-GFP#4, were selected for gradient NaCl treatments. In addition, DAB and NBT staining were performed, and the H2O2 content and catalase (CAT) activity were determined. Then, we used RNA-seq analysis and RT-qPCR to study the mechanism of its tolerance. Results: This study found that after salt treatment, the survival rate and plant height of mtsin1a-1 and mtsin1a-2 were significantly lower than those of the WT. The mutants of MtSIN1a were sensitive to salinity stress. The transgenic alfalfa plants exhibited higher plant height, weaker DAB staining, stronger NBT staining, less H2O2 content, and enhanced CAT activity. The transgenic alfalfa constructed by transforming MtSIN1a showed enhanced salinity tolerance with elevated ROS scavenging. We identified MsSOD1 showing elevated expression levels in transcriptomic analysis. Conclusions: MtSIN1a is a positive regulator for enhancing salinity tolerance in alfalfa with activated ROS scavenging. Full article
(This article belongs to the Special Issue Genetics and Breeding of Forage)
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26 pages, 11108 KB  
Article
Warming in the Maternal Environment Alters Seed Performance and Genetic Diversity of Stylosanthes capitata, a Tropical Legume Forage
by Priscila Marlys Sá Rivas, Fernando Bonifácio-Anacleto, Ivan Schuster, Carlos Alberto Martinez and Ana Lilia Alzate-Marin
Genes 2025, 16(8), 913; https://doi.org/10.3390/genes16080913 - 30 Jul 2025
Viewed by 756
Abstract
Background/Objectives: Global warming and rising CO2 concentrations pose significant challenges to plant systems. Amid these pressures, this study contributes to understanding how tropical species respond by simultaneously evaluating reproductive and genetic traits. It specifically investigates the effects of maternal exposure to [...] Read more.
Background/Objectives: Global warming and rising CO2 concentrations pose significant challenges to plant systems. Amid these pressures, this study contributes to understanding how tropical species respond by simultaneously evaluating reproductive and genetic traits. It specifically investigates the effects of maternal exposure to warming and elevated CO2 on progeny physiology, genetic diversity, and population structure in Stylosanthes capitata, a resilient forage legume native to Brazil. Methods: Maternal plants were cultivated under controlled treatments, including ambient conditions (control), elevated CO2 at 600 ppm (eCO2), elevated temperature at +2 °C (eTE), and their combined exposure (eTEeCO2), within a Trop-T-FACE field facility (Temperature Free-Air Controlled Enhancement and Free-Air Carbon Dioxide Enrichment). Seed traits (seeds per inflorescence, hundred-seed mass, abortion, non-viable seeds, coat color, germination at 32, 40, 71 weeks) and abnormal seedling rates were quantified. Genetic diversity metrics included the average (A) and effective (Ae) number of alleles, observed (Ho) and expected (He) heterozygosity, and inbreeding coefficient (Fis). Population structure was assessed using Principal Coordinates Analysis (PCoA), Analysis of Molecular Variance (AMOVA), number of migrants per generation (Nm), and genetic differentiation index (Fst). Two- and three-way Analysis of Variance (ANOVA) were used to evaluate factor effects. Results: Compared to control conditions, warming increased seeds per inflorescence (+46%), reduced abortion (−42.9%), non-viable seeds (−57%), and altered coat color. The germination speed index (GSI +23.5%) and germination rate (Gr +11%) improved with warming; combined treatments decreased germination time (GT −9.6%). Storage preserved germination traits, with warming enhancing performance over time and reducing abnormal seedlings (−54.5%). Conversely, elevated CO2 shortened GSI in late stages, impairing germination efficiency. Warming reduced Ae (−35%), He (−20%), and raised Fis (maternal 0.50, progeny 0.58), consistent with the species’ mixed mating system; A and Ho were unaffected. Allele frequency shifts suggested selective pressure under eTE. Warming induced slight structure in PCoA, and AMOVA detected 1% (maternal) and 9% (progeny) variation. Fst = 0.06 and Nm = 3.8 imply environmental influence without isolation. Conclusions: Warming significantly shapes seed quality, reproductive success, and genetic diversity in S. capitata. Improved reproduction and germination suggest adaptive advantages, but higher inbreeding and reduced diversity may constrain long-term resilience. The findings underscore the need for genetic monitoring and broader genetic bases in cultivars confronting environmental stressors. Full article
(This article belongs to the Special Issue Genetics and Breeding of Forage)
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20 pages, 5285 KB  
Article
Comparative Analysis of Salt Tolerance and Transcriptomics in Two Varieties of Agropyron desertorum at Different Developmental Stages
by Yuchen Li, Xintian Huang, Xiao Han, Hui Yang and Yan Zhao
Genes 2025, 16(4), 367; https://doi.org/10.3390/genes16040367 - 22 Mar 2025
Cited by 2 | Viewed by 657
Abstract
Background: Most of the grasslands in China are experiencing varying degrees of degradation, desertification, and salinization (collectively referred to as the “three degradations”), posing a serious threat to the country’s ecological security. Agropyron desertorum, known for its wide distribution, strong adaptability, and [...] Read more.
Background: Most of the grasslands in China are experiencing varying degrees of degradation, desertification, and salinization (collectively referred to as the “three degradations”), posing a serious threat to the country’s ecological security. Agropyron desertorum, known for its wide distribution, strong adaptability, and resistance, is an excellent grass species for the ecological restoration of grasslands affected by the “three degradations”. This study focused on two currently popular varieties of A. desertorum, exploring their salt tolerance mechanisms and identifying candidate genes for salt and alkali tolerance. Methods: Transcriptome sequencing was performed on two varieties of A. desertorum during the seed germination and seedling stages under varying degrees of saline–alkali stress. At the seed stage, we measured the germination rate, relative germination rate, germination index, and salt injury rate under different NaCl concentrations. During the seedling stage, physiological indicators, including superoxide dismutase (SOD), peroxidase (POD), malondialdehyde (MDA), proline (PRO), soluble protein (SP), and catalase (CAT), were analyzed after exposure to 30, 60, 120, and 180 mM NaCl for 12 days. Analysis of differentially expressed genes (DEGs) at 6 and 24 h post-treatment with 120 mM NaCl revealed significant differences in the salt stress responses between the two cultivars. Results: Our study indicates that during the seed stage, A. desertorum (Schult.) exhibits a higher relative germination potential, relative germination rate, and relative germination index, along with a lower relative salt injury rate compared to A. desertorum cv. Nordan. Compared with A. desertorum cv. Nordan, A. desertorum (Schult.) has higher salt tolerance, which is related to its stronger antioxidant activity and different antioxidant-related pathways. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were used to identify the key biological processes and pathways involved in salt tolerance, including plant hormone signal transduction, antioxidant defense, and cell membrane stability. Conclusions: A. desertorum (Schult.) exhibits stronger salt tolerance than A. desertorum cv. Nordan. Salt stress at a concentration of 30–60 mM promotes the germination of the seeds of both Agropyron cultivars. The two Agropyron plants mainly overcome the damage caused by salt stress through the AsA-GSH pathway. This study provides valuable insights into the molecular mechanisms of salt tolerance in Agropyron species and lays the groundwork for future breeding programs aimed at improving salt tolerance in desert grasses. Full article
(This article belongs to the Special Issue Genetics and Breeding of Forage)
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